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nf-core/bactmap: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

1.0.0 - Aluminium Spider - 2021-06-18

Initial release of nf-core/bactmap, created with the nf-core template.

The pipeline is composed of the following steps:

  1. Index reference fasta file (BWA index)
  2. Trim reads for quality and adapter sequence (Optional) (fastp)
  3. Estimate genome size (mash sketch)
  4. Downsample fastq files (Optional) (Rasusa)
  5. Variant calling
    1. Read mapping (BWA mem)
    2. Sort and index alignments (SAMtools)
    3. Call and filter variants (BCFtools)
    4. Convert filtered bcf to pseudogenome fasta (vcf2pseudogenome.py)
  6. Create alignment from pseudogenome by concatenating fasta files having first checked that the sample sequences are high quality(calculate_fraction_of_non_GATC_bases.py)
  7. Remove recombination (Optional) (Gubbins)
  8. Extract variant sites from alignment (SNP-sites)
  9. Construct phylogenetic tree (Optional)
    1. Fast/less accurate
    2. Slow/more accurate, maximum likelihood